Online collaborative sharing of documents is typically provided by a network-based file sharing computer system that allows multiple users to access and edit the files. Generally, documents are created and edited by a specific type of native application, such as a word processor or spreadsheet application. Many such applications provide support for tracking comments or other forms of annotation made to portions of a file, such as comments on words, sentences or paragraphs in a document, or cells in a spreadsheet. In these applications, if the portion of the document that is commented upon is deleted, the attached comments are deleted as well. However, existing systems do not provide native programmatic functionality that enables users to create comments or annotations that apply to the entire document, that persist independently of comments made within the file, or that persist when underlying portions of the file are deleted.